Best places to target and visit in Macao for 3 days tour and 1 one day tour in Hongkong.

1. Oh, three days are long enough for you to tour around Macao.
So you are suggested to use two days in Macao and two days in Hong Kong.
Macao:
Day 1:Ruins of St. Paul's, Senado Square, Macau Tower, A-Ma Temple
Day 2:Fisherman's Wharf, Grand Prix Museum, Wine Museum
Hong Kong:
Day 3: Disneyland Resort, Tsim Sha Tsui & A Symphony of Lights
Day 4: Ngong Ping 360 & Big Buddha, Central Area, Causeway Bay

2. About the transportation, you can take the direct ferry at Hong Kong-Macao Ferry Terminal. They depart from 07:00 - 23:59 at intervals of around 15 mins. It costs 164 HKD per person. The duration is about 55 mins.